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- PDB-7niz: Human 14-3-3 sigma in complex with human Estrogen Receptor alpha ... -

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Basic information

Entry
Database: PDB / ID: 7niz
TitleHuman 14-3-3 sigma in complex with human Estrogen Receptor alpha peptide and ligands Fusicoccin-A and WR-1065
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsPROTEIN BINDING / SIGNALING PROTEIN-PEPTIDE complex / Fusicoccin-A / WR-1065
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of epidermal cell division ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of epidermal cell division / epithelial cell proliferation involved in mammary gland duct elongation / protein kinase C inhibitor activity / prostate epithelial cord elongation / positive regulation of epidermal cell differentiation / keratinocyte development / epithelial cell development / keratinization / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / regulation of cell-cell adhesion / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / cAMP/PKA signal transduction / androgen metabolic process / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cellular response to estrogen stimulus / phosphoserine residue binding / mammary gland alveolus development / estrogen response element binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / negative regulation of stem cell proliferation / RNA polymerase II preinitiation complex assembly / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein localization to chromatin / positive regulation of protein localization / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of cell adhesion / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / ESR-mediated signaling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / positive regulation of protein export from nucleus / transcription corepressor binding / negative regulation of protein kinase activity / stem cell proliferation / nuclear estrogen receptor binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / intracellular protein localization / response to estradiol / PIP3 activates AKT signaling / regulation of protein localization / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / regulation of inflammatory response
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. ...14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FUSICOCCIN / WR-1065 / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.48 Å
AuthorsRoversi, P. / Falcicchio, M. / Doveston, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Cooperative stabilisation of 14-3-3 sigma protein-protein interactions via covalent protein modification.
Authors: Falcicchio, M. / Ward, J.A. / Chothia, S.Y. / Basran, J. / Mohindra, A. / Macip, S. / Roversi, P. / Doveston, R.G.
History
DepositionFeb 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8714
Polymers32,0562
Non-polymers8152
Water2,216123
1
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules

A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7418
Polymers64,1114
Non-polymers1,6304
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6430 Å2
ΔGint-44 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.208, 110.938, 62.589
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 31184.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 870.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Thr is phosphorylated / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372
#3: Chemical ChemComp-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12
#4: Chemical ChemComp-UGH / WR-1065


Mass: 134.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5 %Glycerol, 0.19 M Calciumchloridedihydrate, 29% PEG 400, 0.0406 M HEPES pH 7.0, 0.0544 M HEPES pH 7.6
PH range: 7-7.6

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Data collection

DiffractionMean temperature: 170 K / Ambient temp details: cryosteam / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.48→67.074 Å / Num. obs: 33462 / % possible obs: 68 % / Redundancy: 12.9 % / CC1/2: 0.983 / Rmerge(I) obs: 0.499 / Rpim(I) all: 0.144 / Rrim(I) all: 0.52 / Net I/σ(I): 7.3
Reflection shellResolution: 1.48→1.642 Å / Redundancy: 12.9 % / Rmerge(I) obs: 5.126 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 21528 / CC1/2: 0.131 / Rpim(I) all: 1.45 / Rrim(I) all: 5.331 / % possible all: 12.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
BUSTER2.10.3phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JDD

4jdd


Resolution: 1.48→67.07 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.102 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1637 -RANDOM
Rwork0.2108 ---
obs0.2122 33462 68.1 %-
Displacement parametersBiso mean: 25.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.525 Å20 Å20 Å2
2---0.1492 Å20 Å2
3---0.6742 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.48→67.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 56 123 2030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081999HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882707HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d766SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes347HARMONIC5
X-RAY DIFFRACTIONt_it1999HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion266SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1995SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion16.06
LS refinement shellResolution: 1.48→1.58 Å
RfactorNum. reflection% reflection
Rfree0.2508 21 -
Rwork0.2273 --
obs0.228 670 7.71 %
Refinement TLS params.Origin x: -24.5101 Å / Origin y: -17.0315 Å / Origin z: 7.452 Å
111213212223313233
T-0.0582 Å20.0214 Å20.0052 Å2--0.0372 Å20.0078 Å2---0.0358 Å2
L0.495 °2-0.1247 °20.2613 °2-0.9542 °2-0.1091 °2--1.0434 °2
S-0.0235 Å °0.0781 Å °0.0069 Å °0.0781 Å °0.0209 Å °0.0708 Å °0.0069 Å °0.0708 Å °0.0027 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-4 - 231
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION1{ A|* }A401 - 499
4X-RAY DIFFRACTION1{ A|* }A500

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